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The X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase Y253A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WDA PDB ENTRY 2WDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.0M NA FORMATE WITH 20% GLYCEROL AS A CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 4.8 74.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 317.095 α = 90 b = 317.095 β = 90 c = 82.976 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2004-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 59.8 99.9 0.1 6.4 3.1 138108 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 100 0.33 13.2 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2WDA 2.3 158.55 131167 6933 99.94 0.19612 0.19447 0.1934 0.22757 0.2253 RANDOM 24.76
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.11 0.05 0.11 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.087 r_dihedral_angle_4_deg 15.472 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_1_deg 6.682 r_scangle_it 5.043 r_scbond_it 3.287 r_mcangle_it 1.943 r_angle_refined_deg 1.932 r_mcbond_it 1.111 r_chiral_restr 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.087 r_dihedral_angle_4_deg 15.472 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_1_deg 6.682 r_scangle_it 5.043 r_scbond_it 3.287 r_mcangle_it 1.943 r_angle_refined_deg 1.932 r_mcbond_it 1.111 r_chiral_restr 0.165 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11349 Nucleic Acid Atoms Solvent Atoms 841 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing